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Anthropogenic Disturbance and Mojave Desert Tortoise (Gopherus Agassizii) Genetic Connectivity

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Anthropogenic Disturbance and Mojave Desert Tortoise (Gopherus Agassizii) Genetic Connectivity University of Nevada, Reno Connecting the Plots: Anthropogenic Disturbance and Mojave Desert Tortoise (Gopherus agassizii) Genetic Connectivity A dissertation submitted in partial fulfillment of the requirements for the degree Doctor of Philosophy in Geography By Kirsten Erika Dutcher Dr. Jill S. Heaton, Dissertation Advisor May 2020 THE GRADUATE SCHOOL We recommend that the dissertation prepared under our supervision by KIRSTEN ERIKA DUTCHER entitled Connecting the Plots: Anthropogenic Disturbance and Mojave Desert Tortoise (Gopherus agassizii) Genetic Connectivity be accepted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Jill S. Heaton, Ph.D. Advisor Kenneth E. Nussear, Ph.D. Committee Member Scott D. Bassett, Ph.D. Committee Member Amy G. Vandergast, Ph.D. Committee Member Marjorie D. Matocq, Ph.D. Graduate School Representative David W. Zeh, Ph.D., Dean Graduate School May, 2020 i ABSTRACT Habitat disturbance impedes connectivity for native populations by altering natural movement patterns, significantly increasing the risk of population decline. The Mojave Desert historically exhibited high ecological connectivity, but human presence has increased recently, as has habitat disturbance. Human land use primarily occurs in Mojave desert tortoise (Gopherus agassizii) habitat posing risks to the federally threatened species, which has declined as a result. As threats intensify, so does the need to protect tortoise habitat and connectivity. Functional corridors require appropriate habitat amounts and population densities, as individuals may need time to achieve connectivity and find mates. Developments in tortoise habitat have not been well studied, and understanding the relationship between barriers, corridors, population density, and gene flow is an important step towards species recovery. Genetic tools provide a framework to examine processes like movement and incorporating landscape enhances our understanding of genetic patterns. For tortoises a historically connected landscape coupled with limited dispersal produced a pattern of isolation-by-distance. This dissertation highlighted more recent genetic connectivity by: (1) assessing population genetic structure and relatedness across a recently disturbed landscape, (2) evaluating the impact of barriers and corridors using simulations of genetic processes, and (3) investigating the relationship between landscape metrics and genetic connectivity using simulations of disturbance scenarios. I genotyped 299 tortoises at 20 microsatellite loci from the Ivanpah Valley region along the California/Nevada border. A ii fine-scale sampling scheme was applied to evaluate recent gene flow and historical genetic structure. Because the genetic effects of disturbance are often observable after a substantial time lag, I used individually based spatially explicit forward-in-time genetic simulations to test hypotheses related to barriers, population density, and habitat disturbance. I used landscape resistance surfaces representing 17 locations (525 – 625 km2) in southern Nevada and evaluated connectivity success using genetic differentiation. Three genetic clusters that generally corresponded to valleys and one mountain pass were detected with second order relationships up to 60 km apart, suggesting a greater range of interactions than previously suspected. The correlation between pairwise genetic distances and cost distances revealed reduced genetic connectivity across a railway and a highway bisecting the study area. In simulations of linear barriers, genetic connectivity improved with corridors, but was also influenced by population density. Low density landscapes experienced reductions in population size and genetic diversity with or without barriers as the result of individuals moving without finding mates and genetic drift. Simulations found that anthropogenic disturbance increased demographic and genetic effects. Disturbed landscapes with high levels of genetic connectivity tended towards low levels of landscape fragmentation with high amounts of suitable habitat. Urban growth is predicted to exacerbate declines in tortoise populations and genetic connectivity unless intact habitat and populations are adequately protected and connected. This research provides a basis for management actions to protect desert tortoise habitat between existing conservation blocks and restore connectivity along current barriers. iii ACKNOWLEDGEMENTS “Look closely at nature. Every species is a masterpiece, exquisitely adapted to the particular environment in which it has survived. Who are we to destroy or even diminish biodiversity?” – E.O. Wilson This work is dedicated to the Mojave desert tortoise. It was informed, molded, and enthusiastically supported by many individuals, to whom I am grateful. My committee members collectively formed a rigorous scientific team that transformed me from a field biologist into a researcher, and modeled collaboration through their interactions with one another. My major professor, Jill Heaton expertly managed our group, ensuring I never stumbled too far in the weeds. She led me into the fold of academia and believed I could accomplish this goal from our first interview. I am truly fortunate to have been given this opportunity. Kenneth Nussear challenged me to think in ways I never imagined possible and would not tolerate the possibility of defeat. He allowed me the freedom to explore and I cannot imagine reaching this point without his instruction. Amy Vandergast coached me along the path of population genetics, always constructive in her criticism, she helped me expand my knowledge, and is an excellent role model. Marjorie Matocq immersed me in theory and found something positive in my work before gently redirecting me to improve. I am thankful for her every kindness and critique. Scott Bassett showed genuine enthusiasm for this work and engaged me in diverse perspectives. I also offer my appreciation for Todd Esque, whose collaboration led me to iv consider wider views, broader implications, and the back story that led us here. He was always willing to discuss, listen, and advocate for this research. This dissertation began as part of a larger project on conservation corridors for desert tortoises. I would like to thank the principal investigators Ken Nussear, Todd Esque, and Amy Vandergast for entrusting me with a portion of this important work. Activities associated with desert tortoise handling were permitted through the U.S. Fish and Wildlife Service (Roy Averill-Murray), Nevada Division of Wildlife (Christy Klinger), and California Department of Fish and Wildlife (Rebecca Jones). The Bureau of Land Management (Amy Fesnock and Mark Slaughter), Clark County Desert Conservation Program (Scott Cambrin and Kimberley Jenkins), and the National Fish and Wildlife Federation (Eliza Braendel and Anne Butterfield) funded this research, and I thank them for their contributions. The University of Nevada, Reno (UNR) Department of Geography, Graduate Student Association, and Mackay Scholar Award provided academic funding. I appreciate the Department of Geography office staff for assisting with administrative details. I am immensely grateful to U.S. Geological Survey for field support and invaluable feedback. It was an honor to work with such a dedicated bunch of tireless biologists, led by Todd Esque. Thank you to Felicia Chen for her exceptional organizational skills, attention to detail, willingness to help, and honesty. Kristina Drake provided invaluable professional advice, talking sense to me when I needed it most. I admire Ben Gottsacker for his work ethic, ability to traverse difficult terrain, and humility. I also credit him with turning me into a Green Bay Packers fan even though I do v not watch football. I appreciate Amanda McDonald for her calm approach and reserved dignity. I always looked forward to working with her. Jordan Swart showed continual enthusiasm, accomplishing the task at hand with a quiet focus and positive outlook. Special thanks to Sara Murray, not only is she filled with scientific inquiry, she is resourceful and once saved me considerable time and embarrassment when I locked my keys in my vehicle. I am thankful for the efforts of: Patrick Baird, Molly Bechtel, Lesley DeFalco, Sasha Karosas, Sydney Kelly, Kathy Longshore, Nan Nourn, Jon O’Hearn, Greg Olson, Megan Rabinowich, and Matt Simes. Field surveys were conducted by Tim Alvey, Kemp Anderson, Laina Baltic, Mary Baker, Chrystal Bedwell, Kelsi Black, Chris Blandford, Corey Chan, Lehong Chow, Don Copeland, Gene Drollinger, Chris Fabry, Kelly Herbinson, Kathryn Hilsinger, Danna Hinderle, Kelly Hunt, Michael Honer, Audrey Johnson, Chereka Keaton, Kristin Koeper, Colden McClurg, Corey Mitchell, Jake Mohlman, Freya Reder, Mike Sally, Brian Sandstrom, Chris Scanlan, Kyle Shelp, Crissy Slaughter, Kathy Simon, Adam Walters, Carrie Warman, Rachel Woodard, and John Yerger. Additional samples were graciously provided by Kristina Drake, Todd Esque, and Rachel Woodard. Many thanks to Lee Bice (Clark County Desert Conservation Program) for providing GIS layers. I appreciate everyone who instructed me in the technical details and made sure I was up to speed. First and foremost, Anna Mitelberg for her tremendous patience. She is an amazing teacher and trusted friend. Amy Vandergast generously allowed the use of her genetics lab. Mary Peacock and Veronica Kirchoff provided an introduction to extractions. Ken Nussear, Devin Jacobs, Kevin Shoemaker, and Margarete Walden led
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